Merge pull request #200 from Steinbeck-Lab/dev-kohulan

feat: add depict router #194 and #199

app/main.py

@@ -2,7 +2,7 @@
 from fastapi.responses import RedirectResponse
 from fastapi_versioning import VersionedFastAPI
 
-from .routers import chem, converters, decimer
+from .routers import chem, converters, depict, ocsr
 from fastapi.middleware.cors import CORSMiddleware
 
 from prometheus_fastapi_instrumentator import Instrumentator
@@ -34,7 +34,8 @@
 
 app.include_router(chem.router)
 app.include_router(converters.router)
-app.include_router(decimer.router)
+app.include_router(depict.router)
+app.include_router(ocsr.router)
 
 app = VersionedFastAPI(
     app,

app/modules/toolkits/rdkitmodules.py

@@ -212,3 +212,20 @@ def get2Dmol(smiles: str):
         return molfile
     else:
         return "Error reading SMILES string, check again."
+
+
+def getRDKitCXSMILES(smiles: str):
+    """This function takes an input as a SMILES string and
+    returns a CXSMILES with coordinates.
+    Args (str): SMILES string.
+    Returns (str): CXSMILES with coordinates.
+    """
+    if any(char.isspace() for char in smiles):
+        smiles = smiles.replace(" ", "+")
+    mol = Chem.MolFromSmiles(smiles)
+
+    if mol:
+        AllChem.Compute2DCoords(mol)
+        return Chem.MolToCXSmiles(mol)
+    else:
+        return "Error reading SMILES string, check again."

app/routers/chem.py

@@ -1,21 +1,19 @@
-from fastapi import Body, Request, APIRouter
+from fastapi import Body, APIRouter
 from typing import Optional
 from typing_extensions import Annotated
 from rdkit import Chem
 from rdkit.Chem.EnumerateStereoisomers import (
     EnumerateStereoisomers,
 )
 from chembl_structure_pipeline import standardizer, checker
-from fastapi.responses import Response, HTMLResponse, JSONResponse
+from fastapi.responses import Response, JSONResponse
 from app.modules.npscorer import getNPScore
 from app.modules.classyfire import classify, result
 from app.modules.toolkits.cdkmodules import (
     getTanimotoSimilarityCDK,
     getCDKHOSECodes,
 )
-from app.modules.depict import getRDKitDepiction, getCDKDepiction
 from app.modules.toolkits.rdkitmodules import (
-    get3Dconformers,
     getTanimotoSimilarityRDKit,
     getRDKitHOSECodes,
 )
@@ -148,24 +146,6 @@ async def ClassyFire_result(id: str):
         return data
 
 
-@router.get("/rdkit3d")
-async def RDKit3D_Mol(smiles: str):
-    """
-    Generate 3D Coordinates using RDKit and return the mol block.
-
-    - **SMILES**: required (query)
-    """
-    if smiles:
-        mol = Chem.MolFromSmiles(smiles)
-        if mol:
-            return Response(
-                content=get3Dconformers(smiles).replace("$$$$\n", ""),
-                media_type="text/plain",
-            )
-        else:
-            return "Error reading SMILES string, check again."
-
-
 @router.get("/tanimoto")
 async def Tanimoto_Similarity(smiles: str, toolkit: Optional[str] = "cdk"):
     """
@@ -194,38 +174,6 @@ async def Tanimoto_Similarity(smiles: str, toolkit: Optional[str] = "cdk"):
         return 'Please give a SMILES pair with "," separated. (Example: api.naturalproducts.net/chem/tanimoto?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C,CN1C=NC2=C1C(=O)NC(=O)N2C)'
 
 
-@router.get("/depict")
-async def Depict2D_molecule(
-    smiles: str,
-    generator: Optional[str] = "cdksdg",
-    width: Optional[int] = 512,
-    height: Optional[int] = 512,
-    rotate: Optional[int] = 0,
-    CIP: Optional[bool] = False,
-    unicolor: Optional[bool] = False,
-):
-    """
-    Generate 2D Depictions using CDK or RDKit using given parameters.
-
-    - **SMILES**: required (query)
-    - **generator**: optional (defaults: cdk)
-    - **width**: optional (defaults: 512)
-    - **height**: optional (defaults: 512)
-    - **rotate**: optional (defaults: 0)
-    """
-    if generator:
-        if generator == "cdksdg":
-            return Response(
-                content=getCDKDepiction(smiles, [width, height], rotate, CIP, unicolor),
-                media_type="image/svg+xml",
-            )
-        else:
-            return Response(
-                content=getRDKitDepiction(smiles, [width, height], rotate),
-                media_type="image/svg+xml",
-            )
-
-
 @router.get("/checkerrors")
 async def Check_Errors(smiles: str, fix: Optional[bool] = False):
     """
@@ -272,27 +220,25 @@ async def Check_Errors(smiles: str, fix: Optional[bool] = False):
         return "Error reading SMILES string, check again."
 
 
-@router.get("/depict3D", response_class=HTMLResponse)
-async def Depict3D_Molecule(
-    request: Request,
+@router.get("/hosecode")
+async def HOSE_Codes(
     smiles: str,
+    spheres: int,
+    toolkit: Optional[str] = "cdk",
+    ringsize: Optional[bool] = False,
 ):
     """
-    Generate 3D Depictions using RDKit.
+    Generates HOSE Codes using CDK/RDKit.
 
     - **SMILES**: required (query)
+    - **spheres**: required (query)
+    - **toolkit**: Optional (default:CDK)
+    - **ringsize**: Optional (default:False)
     """
     if smiles:
-        content = {"request": request, "molecule": get3Dconformers(smiles)}
-        return templates.TemplateResponse("mol.html", content)
-
-
-@router.get("/hosecode")
-async def HOSE_Codes(framework: str, smiles: str, spheres: int, ringsize: bool = False):
-    if smiles:
-        if framework == "cdk":
+        if toolkit == "cdk":
             return await getCDKHOSECodes(smiles, spheres, ringsize)
-        elif framework == "rdkit":
+        elif toolkit == "rdkit":
             return await getRDKitHOSECodes(smiles, spheres)
     else:
         return "Error reading SMILES string, check again."

app/routers/converters.py

@@ -11,7 +11,11 @@
     getCanonSMILES,
     getInChI,
 )
-from app.modules.toolkits.rdkitmodules import get3Dconformers, get2Dmol
+from app.modules.toolkits.rdkitmodules import (
+    get3Dconformers,
+    get2Dmol,
+    getRDKitCXSMILES,
+)
 from app.modules.toolkits.openbabelmodules import (
     getOBMol,
     getOBCanonicalSMILES,
@@ -124,12 +128,12 @@ async def SMILES_to_InChI(smiles: str, generator: Optional[str] = "cdk"):
         if generator:
             if generator == "cdk":
                 return str(getInChI(smiles))
-        elif generator == "rdkit":
-            mol = Chem.MolFromSmiles(smiles)
-            if mol:
-                return Chem.inchi.MolToInchi(mol)
-        elif generator == "openbabel":
-            return getOBInChI(smiles)
+            elif generator == "rdkit":
+                mol = Chem.MolFromSmiles(smiles)
+                if mol:
+                    return Chem.inchi.MolToInchi(mol)
+            elif generator == "openbabel":
+                return getOBInChI(smiles)
         else:
             return "Error reading SMILES string check again."
     else:
@@ -149,20 +153,20 @@ async def SMILES_to_InChIKey(smiles: str, generator: Optional[str] = "cdk"):
         if generator:
             if generator == "cdk":
                 return str(getInChI(smiles, InChIKey=True))
-        elif generator == "rdkit":
-            mol = Chem.MolFromSmiles(smiles)
-            if mol:
-                return Chem.inchi.MolToInchiKey(mol)
-        elif generator == "openbabel":
-            return getOBInChI(smiles, InChIKey=True)
+            elif generator == "rdkit":
+                mol = Chem.MolFromSmiles(smiles)
+                if mol:
+                    return Chem.inchi.MolToInchiKey(mol)
+            elif generator == "openbabel":
+                return getOBInChI(smiles, InChIKey=True)
         else:
             return "Error reading SMILES string check again."
     else:
         return "Error reading SMILES string check again."
 
 
 @router.get("/cxsmiles")
-async def SMILES_to_CXSMILES(smiles: str):
+async def SMILES_to_CXSMILES(smiles: str, generator: Optional[str] = "cdk"):
     """
     Convert SMILES to CXSMILES:
 
@@ -171,8 +175,12 @@ async def SMILES_to_CXSMILES(smiles: str):
     if any(char.isspace() for char in smiles):
         smiles = smiles.replace(" ", "+")
     if smiles:
-        cxsmiles = getCXSMILES(smiles)
-        return cxsmiles
+        if generator:
+            if generator == "cdk":
+                cxsmiles = getCXSMILES(smiles)
+                return cxsmiles
+            else:
+                return getRDKitCXSMILES(smiles)
     else:
         return "Error reading SMILES string check again."
 

app/routers/depict.py

@@ -0,0 +1,67 @@
+from fastapi import Request, APIRouter
+from typing import Optional
+from fastapi.responses import Response, HTMLResponse
+from app.modules.depiction import getRDKitDepiction, getCDKDepiction
+from app.modules.toolkits.rdkitmodules import get3Dconformers
+from fastapi.templating import Jinja2Templates
+
+templates = Jinja2Templates(directory="app/templates")
+
+router = APIRouter(
+    prefix="/depict",
+    tags=["depict"],
+    dependencies=[],
+    responses={404: {"description": "Not found"}},
+)
+
+
+@router.get("/")
+async def depict_index():
+    return {"module": "depict", "message": "Successful", "status": 200}
+
+
+@router.get("/2D")
+async def Depict2D_molecule(
+    smiles: str,
+    generator: Optional[str] = "cdksdg",
+    width: Optional[int] = 512,
+    height: Optional[int] = 512,
+    rotate: Optional[int] = 0,
+    CIP: Optional[bool] = False,
+    unicolor: Optional[bool] = False,
+):
+    """
+    Generate 2D Depictions using CDK or RDKit using given parameters.
+
+    - **SMILES**: required (query)
+    - **generator**: optional (defaults: cdk)
+    - **width**: optional (defaults: 512)
+    - **height**: optional (defaults: 512)
+    - **rotate**: optional (defaults: 0)
+    """
+    if generator:
+        if generator == "cdksdg":
+            return Response(
+                content=getCDKDepiction(smiles, [width, height], rotate, CIP, unicolor),
+                media_type="image/svg+xml",
+            )
+        else:
+            return Response(
+                content=getRDKitDepiction(smiles, [width, height], rotate),
+                media_type="image/svg+xml",
+            )
+
+
+@router.get("/3D", response_class=HTMLResponse)
+async def Depict3D_Molecule(
+    request: Request,
+    smiles: str,
+):
+    """
+    Generate 3D Depictions using RDKit.
+
+    - **SMILES**: required (query)
+    """
+    if smiles:
+        content = {"request": request, "molecule": get3Dconformers(smiles)}
+        return templates.TemplateResponse("mol.html", content)

app/routers/decimer.py → app/routers/ocsr.py

@@ -9,16 +9,16 @@
 from app.modules.decimermodules import getPredictedSegments
 
 router = APIRouter(
-    prefix="/decimer",
-    tags=["decimer"],
+    prefix="/ocsr",
+    tags=["ocsr"],
     dependencies=[],
     responses={404: {"description": "Not found"}},
 )
 
 
 @router.get("/")
-async def DECIMER_Index():
-    return {"module": "decimer", "message": "Successful", "status": 200}
+async def ocsr_index():
+    return {"module": "ocsr", "message": "Successful", "status": 200}
 
 
 @router.post("/process")